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Yorodumi- PDB-7cj2: Crystal structure of the Fab antibody complexed with human YKL-40 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cj2 | ||||||
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Title | Crystal structure of the Fab antibody complexed with human YKL-40 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Chitin binding protein / Inflammatory response / Fab / antibody-antigen complex / APOPTOSIS | ||||||
Function / homology | Function and homology information activation of NF-kappaB-inducing kinase activity / chitin binding / cellular response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / inflammatory response ...activation of NF-kappaB-inducing kinase activity / chitin binding / cellular response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / inflammatory response / apoptotic process / endoplasmic reticulum / extracellular space Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Choi, S. / Na, J.H. / Lee, S.J. / Woo, J.R. / Kim, D.Y. / Hong, J.T. / Lee, W.K. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the Fab antibody complexed with human YKL-40 Authors: Choi, S. / Na, J.H. / Lee, S.J. / Woo, J.R. / Kim, D.Y. / Lee, W.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cj2.cif.gz | 373.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cj2.ent.gz | 241.9 KB | Display | PDB format |
PDBx/mmJSON format | 7cj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cj2_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7cj2_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7cj2_validation.xml.gz | 56.6 KB | Display | |
Data in CIF | 7cj2_validation.cif.gz | 79.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/7cj2 ftp://data.pdbj.org/pub/pdb/validation_reports/cj/7cj2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Antibody , 2 types, 4 molecules CKDL
#1: Antibody | Mass: 23128.824 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21[DE3] #2: Antibody | Mass: 23407.951 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21[DE3] |
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-Protein / Non-polymers , 2 types, 211 molecules AB
#3: Protein | Mass: 40536.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHI3L1, hCG_24326 / Production host: Homo sapiens (human) / References: UniProt: A0A024R969 #6: Water | ChemComp-HOH / | |
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-Sugars , 2 types, 2 molecules
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.4 % |
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Crystal grow | Temperature: 293.15 K / Method: microbatch / pH: 6.5 Details: 0.6M Sodium Chloride, 0.1M MES:NaOH, pH 6.5, 20% (w/v)PEG 4000, 1.0M NDSB-256 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→45.83 Å / Num. obs: 70738 / % possible obs: 99.84 % / Redundancy: 6.8 % / Biso Wilson estimate: 64.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.45→2.48 Å / Rmerge(I) obs: 0.07466 / Num. unique obs: 70634 / CC1/2: 0.999 / CC star: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HJX,5VEB Resolution: 2.7→45.83 Å / SU ML: 0.4011 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.0523 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→45.83 Å
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Refine LS restraints |
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LS refinement shell |
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